The Starks are "done", but either way Bolton wants all of them dead, so they aren't as worthless as they seem. It has been established that they have always ruled the north, so who knows, maybe their name still carries weight, and are a threat to whomever wants to rule those lands (which are about to be overcome by wild-lings and zombies anyway.
The Vale hasn't been a player till now because it's pretty obvious they prefer to be holed up inside their keep, but with Littlefinger there things might change. We don't know their forces or what they can be capable of with someone like him in charge.
I still think that roose bolton is enough of a prick that living in a region ruled by him would have to suck. "Support the return of the starks! Less shitty than that bolton asshole!" Could make for a decent rallying cry to drag parts of the north to another side if a stark-affiliated house ever gains any momentum again.
Also if, say, the umbers are good enough friends to hide rickon, they'd be enthusiastic about joining the house bolton haters club even if his rule turns out to be not oppressive. Maybe there are more houses like that.
Or maybe littlefinger doesn't give a fuck about the outside world and is content to hide in the vale being creeped on by lysa while creeping on sansa in turn. Just seems like that'd be a disappointing endgame for the amount of effort he's gone through.
Don't really know who else would wind up pro-stark. Tyrells get burnt out on the lannisters and change side? They seem pretty committed to non-violent gameplay. Dorne rebels? Doesn't seem impossible, actually.... stannis would be pro-stark if he thought they'd bend the knee but he is now dead on the inside after the blackwater and Icant imagine him having enough power to wage a one-house war any longer.
Maybe someday, a decade from now, when danerys finally stumbles into westeros in a firey purge, she'll decide to put a stark into neo-winterfell. With what she's done to the slavers, id imagine that she'll be on enough of a power trip if she makes it that far to take a more aggressive arbiter-of-justice stance... which in my mind would involve feeding the freys, boltons, and at least tywin, cersei and jaime to her dragons.
I can't even remember what state the riverlands are in right now. Tullys are useless yeah?
Side note: shit. I just realized. Dany is the only character whose death I cannot imagine happening. She must be screwed.